Scanning electron microscopes (SEMs) are often used in semiconductor fabrication plants to scan patterned wafers to obtain images from selected subregions that provide information on process quality. SEMs provide much better resolution than optical microscopes, because electrons have much smaller wavelength compared to optical light. However, SEMs are comparatively slow at imaging due to their sequential scanning nature. Multi-column arrays with parallel imaging capabilities improve the imaging speed of the SEMs, but even an array of 100 columns can only scan up to 1% of wafer area per hour, which is much less than what is needed by the industry. This means that sampling only selected subregions of the wafer, instead of performing a full wafer scan, becomes the practical solution. In this case the full wafer must be completely covered by the field of view of the column array so that selected areas for scanning are exposed to the electron beams. Some critical features on the wafer will not be covered if the full wafer cannot be covered by the field of view of all columns in a given time, say one hour. Therefore, an innovative method for a multi-column array is required in order to be able to reach all critical points. Because an electron beam inspection system is usually integrated with a waveform generator, it can also do pattern lithography on wafers, with proper software control.